On 01/16/2018 06:43 AM, Dimitri Maziuk wrote: > On 01/15/2018 02:43 PM, Tim Dudgeon wrote: > >> Could there be something in a more general project to bridge the >> compound (mol/smiles), sequence (protein/nucleotide seq + alignments) >> and structure (pdb/mmcif/mmtf) worlds? > > FWIW PDB builds everything up from structure because they can derive > bonds from the coordinates and that's the only way you can do it in the > code. Without bonds, trying to link compounds in a sequence doesn't > really work even if you have two cysteins in a bog standard protein > sequence, with generic compounds it gets too hard fast. > > PDB has in the mmCIF chem. comp. model "leaving atom flag" that marks > *a* bonding site but it doesn't tell you what kind of bond can form > there, nor what to do if there's more than one. You need a whole lot of > other code to figure out how to link two compounds into a sequence.
Chimera can do the PDB to MOL2 conversion (so there might be some code to look at since UCSF Chimera is open source). If you want their algorithm, I think it is in there: @article {JCC:JCC540120716, author = {Meng, Elaine C. and Lewis, Richard A.}, title = {Determination of molecular topology and atomic hybridization states from heavy atom coordinates}, journal = {Journal of Computational Chemistry}, volume = {12}, number = {7}, publisher = {John Wiley & Sons, Inc.}, issn = {1096-987X}, url = {http://dx.doi.org/10.1002/jcc.540120716}, doi = {10.1002/jcc.540120716}, pages = {891--898}, year = {1991}, } > And then there's structure calculation that I don't know if there's > anything that works on not proteins, or can predict disordered regions > well etc. > > If anyone's counting votes, pretty 2D depictions get mine. > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss